I'll be using either PokeGen or PokeSav to create some legendary pokemon on Pokemon Black, some pokemon from 5th Generation and some from earlier generatins, Which one is better to do what I just mentioned?

Pokegen to make the Pokemon from scratch. You should still open the save file in Pokesav to give the Pokemon your Secret ID. Otherwise it will still trigger the "fake" crap if you're using your Trainer ID... seems to not like adding your Secret ID to your Pokemon
Pokegen is rather nice. Pokesav is just as good and deserves just as much respect as Pokegen.